Agave nectar makers such as Wholesome Sweeteners, and companies like Brain Toniq which use agave nectar in their products, have fired back at detractors, defending against accusations of contamination with pesticides and other synthetic chemicals. Natural food and nutrition websites have weighed in on both sides of the issue, and everyone has an opinion. I'm not a doctor, nutritionist, or dietitian, but I'm a pretty good reader, so here's what I've found out, in short:
What the nay-sayers say
Agave nectar isn't a "nectar" at all—it is a sugar syrup manufactured largely from starch. The agave is a huge spiky plant up to 12 feet in diameter, and to harvest it they cut off all the leaves and press the resulting bulbous stem (the "piña," so-called because it resembles a pineapple) to release a starchy juice. This juice is heat-treated or cracked with enzymes to hydrolyze the starch into fructose and sucrose, and the resulting syrup is boiled down to thicken it. This process is very similar to the process of creating syrup from corn starch, therefore all the same health issues that arise from eating high fructose corn syrup also apply to agave nectar. Agave nectar is made using sulfuric and/or hydrofluoric acids, and a number of unpalatable filtration and clarifying chemicals. Unscrupulous and unregulated Mexican growers are providing agave nectar that is contaminated with pesticides and high levels of naturally occurring saponins, which may possibly cause miscarriage, and also a carcinogen called hydroxymethylfurfural. The agave syrup is sweeter than table sugar because it has more fructose in it, and we perceive fructose as sweeter than sucrose. Although fructose has a low glycemic index and does not spike blood glucose levels like other sugars, this is because it is processed differently in the liver and is turned into "organ fat" that is really bad for you.
Creating sugar from starch via the use of heat is a common process, and happens in your kitchen every time you cook a sweet potato or other starchy vegetable like beets, potatoes, and squash.
Creating high fructose corn syrup involves many more chemical agents than creating agave syrup, and organic agave is not treated with pesticides and is not genetically engineered like the corn supply in the USA is. The production of organic agave syrup does not involve sulfuric or hydrofluoric acid.
Agave syrup is filtered using activated charcoal, which is simple carbon and is used in any household water filtration system. It is also filtered using diatomaceous earth, which is a safe and inert silica sand made up of the fossil skeletons of blue-green algae.
Saponins are found in all sorts of foods besides agave—they are in spinach, grapes, nuts, beans, and seeds, and the amount of saponins found in agave are equal to the amount found in lentils.
Hydroxymethylfurfural is a fancy name for caramelization—what happens when you expose a sugar to heat; it's the telltale brown color of food that has been cooked by any other process than boiling or steaming.
Fructose is not bad for you in and of itself, but like all sweeteners it should be taken in moderation.
People get upset when they are accused of trading the health and wellbeing of their fellow humans to make a buck—and the organic agave nectar makers are understandably unhappy with what they see as an unmerited attack on their products, which provide vegetarian- and vegan-friendly sweetness to baked goods and drinks.
Dr. Mercola has been accused by business, scientific, and medical communities of using scare tactics to drive commerce to his own sites and products, and has been criticized for making unsubstantiated claims and recommendations for dietary supplements. On the other hand, some sites do claim untruthfully that agave nectar is "safe for diabetics" because of its low glycemic index.
While the makers of organic agave nectar are rigorous in their product quality assurance procedures, the term "agave nectar" is not closely defined or controlled by the FDA and may be unscrupulously used by businesses interested more in making money and less in public health.
"Free" fructose, consumed outside of eating a piece of fruit, and especially when consumed in large quantities, really has been associated with non-alcoholic fatty liver syndrome and a host of other health problems.
Do your homework, and consume agave nectar and foods sweetened with it in extreme moderation, and you should be fine. My take on the issue is that it's a human failing more than anything else: We all love sweet-tasting food, and we are all susceptible to the false promise of a "free lunch"—a sweetener that we can eat as much as we want without suffering ill health as a result. I'm afraid that such a thing just doesn't exist. Most sugars cause blood glucose spikes, and studies of fructose have shown it to increase blood triglycerides, to increase the feeling of residual hunger after a meal, and to be associated with a substantial risk of developing gout.
Don't even get me started on artificial sweeteners like sucralose and Aspartame! Sugar alcohols like sorbitol, mannitol, and xylitol can cause bloating and diarrhea, and xylitol sensitivity can cause mouth ulcers in a small percentage of the population. Even stevia may cause mild nausea if taken in too large an amount. Get a handle on your sweet tooth by moderating your intake of sweet foods, and you will find you'll need less sweetness to satisfy yourself, and then it doesn't matter so much what sweetener you use.